owl/Athaliana/20180925_oly_RNAseq_genome_hisat2

Alignment of Olympia oyster RNAseq data to Olympia oyster genome (Olurida_v081) using HISAT2.

In preparation for genome coverage bedgraph.

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FILES:

- 20180925_Olurida_v081.bam: BAM file, converted from original SAM file, using SAMtools.

- 20180925_Olurida_v081.sam: HISAT2 SAM file alignment output.

- 20180925_Olurida_v081.sorted.bam: Sorted BAM file.

- 20180925_Olurida_v081.sorted.bam.bai: Sorted and indexed BAM file for IGV usage.

- 20180925_oly_RNAseq_genome_hisat2.sh: SBATCH Mox script. Contains commands and list of input files for HISAT2 RNAseq alignment to Olurida_v081 genome. Includes commands for indexing genome. SAMtools sorting and indexing commands for the BAM file contained a typo. Those commands were subsequently executed in another script (20180925_oly_RNAseq_genome_sort_bam.sh).

- 20180925_oly_RNAseq_genome_sort_bam.sh: SBATCH Mox script. Contains commands for SAMtools sorting and indexing.

- *ht*: HISAT2 genome index files.

- slurm-322174.out: SLURM output file from 20180925_oly_RNAseq_genome_hisat2.sh.

- slurm-322409.out: SLURM output file from 20180925_oly_RNAseq_genome_sort_bam.sh.

- system_path.log: A text file attempting to document various program versions being used by Mox.